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Table 1 Oligonucleotides used for PCR amplification of viral and transgene sequences

From: Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues

Primer Sequence (5'-3') Target sequence
EAB555/F (5'-TACATCGGCCTTTGAGTCGCATGG-3') EACMV DNA B
EAB555/R (5'-CTTATTAACGCCTATATAAACACC-3') EACMV DNA B
JSP001 (5'-ATGTCGAAGCGACCAGGAGAT-3') ACMV (AV1/CP)
JSP002 (5'-TGTTTATTAATTGCCAATACT-3') ACMV (AV1/CP)
UniF (5'-KSGGGTCGACGTCATCAATGACGTTRTAC-3') CMGs DNA A
UniR (5'-AARGAATTCATKGGGGCCCARARRGACTGGC-3') CMGs DNA A
MSVF (5'-ATCCCTCCAAATTCCGACAC-3') MSV
MSVR (5'-TCCATGTACAAAGCTCCTCT-3') MSV
C1F (5'-GCAGATCTATGCCTCGTTTATTTAAAATATATGC-3') TYLCV
C1R (5'-GCGGTACCTTACGCCTTATTGGTTTCTTCTTGGC-3') TYLCV
TMVF (5'-GCGGTGGCGGCCGATCCATGGAACTTACAG-3') TMV
TMVR (5'-GATTCGAACCCCTCGCTTTAT-3') TMV
POT1 (5'-gacgaattcTGYGAYGCBGATGGYTC-3') TEV & PVY
POT2 (3'-ACCACRTADCTBTTAcctaggtcag-5') TEV & PVY
AC1F (5'-ATGAGAACTCCTCGTTTTAGAA-3') ACMV-Kenya AC1
AC1R (5'-ATGAGAACTCCT CGTTTTAGAA-3') ACMV-Kenya AC1
MP141 (5'-ATGATTGAACAAGATGGATTGCAC-3') Npt II coding sequence
MP142 (5'-TCAGAAGAACTCGTCAAGAAGGCG-3') Npt II coding sequence
  1. EACMV – East African cassava mosaic virus; ACMV – African cassava mosaic virus; MSV – maize streak virus; TYLCV – tomato yellow leaf curl virus; TMV – tobacco mosaic virus; TEV – tobacco etch virus; PVY – potato virus Y
  2. EAB555/F &EAB555/R: PCR conditions consisted of 30 cycles of 94°C for 1 min, 58°C for 1 min. and 72°C for 2 mins.
  3. JSP001 &JSP002: PCR conditions consisted of 30 cycles of 94°C for 1 min, 45°C for 1 min. and 72°C for 2 mins.
  4. Uni F &Uni R: K = G + T, R = A + G, S = G + C. PCR conditions consisted of 30 cycles of 94°C for 1 min., 58°C for 1 min. and 72°C for 2 min.
  5. MSV F &MSVR : PCR conditions consisted of 30 cycles of 94°C for 1 min, 59°C for 1 min and 72°C for 2 mins.
  6. C1F &C2R: PCR conditions consisted of 94°C for 10 mins followed by 35 cycles of 94°C for 30 secs., 60°C for 1 min and 72°C for 1.5 mins followed and extension of 7 mins at 72°C.
  7. AC1F &AC1R : PCR conditions consisted 94°C of 5 mins followed by 35 cycles of 94°C for 30 secs, 58°C for 1 min. and 72°C for 1 mins followed by extension of 10 mins at 72°C.
  8. MP141 &MP142: PCR conditions consisted 5 mins. at 94°C followed by 35 cycles of 94°C for 30 secs, 58°C for 1 min. and 72°C for 1 mins. followed by extension time of 10 mins. at 72°C.